1. Field of the Invention
This invention relates to the methods and compositions suitable for the detection, analysis, quantitation and sequencing of double stranded nucleic acids.
2. Description of the Related Art
A. Invasion of Double Stranded Nucleic Acid.
Linear, non-supercoiled double-stranded DNA (dsDNA) is known to be able to accommodate an additional oligonucleotide strand with much less efficiency as compared with single-stranded nucleic acids and supercoiled DNAs. Formation of intermolecular triplexes is mostly limited to long homopurine-homopyrimidine regions (See: Frank-Kamenetskii, M. D., & Mirkin, S. M. (1995) Annu. Rev. Biochem. 64, 65-95 and Soyfer, V. N. & Potaman, V. N. (1996) Triple-Helical Nucleic Acids (Springer, N.Y.). D-loops are formed in linear dsDNA only at the ends of the DNA duplex and when using long single-stranded DNA molecules (See: Wetmur, J. G. (1991) Critical Rev. Biochem. Mol. Biol. 26, 227-259). R-loops may be formed inside linear dsDNA, but long RNAs and transient DNA denaturation is required (See: Thomas, M., White, R. L., & Davis, R. W. (1976) Proc. Natl. Acad. Sci. USA 73, 2294-2298). A complex between an oligodeoxynucleotide (ODN) and linear dsDNA can be formed with the assistance of the RecA protein. However, the fidelity of recognition of this complex is lower as compared with the protein-free DNA-DNA. Moreover, the complex is unstable upon deproteinization (See: West, S. C. (1992) Annu. Rev. Biochem. 61, 603-640 and Malkov, V. A., Sastry, L. & Camerini-Otero, R. D. (1997) J. Mol. Biol. 271, 168-177). It has recently been demonstrated that a pair of complementary modified ODNs will bind to dsDNA as a result of their self-mediated invasion of the DNA duplex. However, these complexes were formed only at the ends of linear dsDNA (See: Kutyavin, I. V., Rhinehart, R. L, Lukhtanov, E. A, Gom, V. V., Meyer, R. B., Jr., & Gamper, H. B., Jr. (1996) Biochemistry 35, 11170-11176). In addition, a few techniques exist for the formation of specific complexes between ODNs and dsDNA based upon either prior DNA denaturation or degradation of one DNA strand before ODN binding. These techniques, however, require subsequent reconstruction or reparation of the DNA duplex (See: Shepard, A. R., & Rae, J. L. (1997) Nucleic Acid Res. 25, 3183-3185 and Anonymous (1997/1998) in Gibco BRL Products & Reference Guide, (Life Technologies, Gaithersburg, Md.), pp. 1914-1915).
B. Sequencing Double Stranded Nucleic Acids.
Progress in enzymatic (or dideoxy) DNA sequencing has (See: Sanger, F., Nicklden, S. and Coulson, A. R. (1977) Proc. Nat. Acad. Sci. USA 74, 5463-5467) completely changed the science of molecular genetics and revolutionized the field of modern biotechnology. However, the development of improved dideoxy sequencing methodologies as well as the introduction of new sequencing approaches promises to further facilitate great advancements in science.
High quality sequence data is generally obtained using dideoxy sequencing reactions on purified single-stranded (ss) DNA templates. Consequently, Sanger sequence typically requires the performance of laborious ssDNA isolation (See: Griffin, H. G. and Griffin, A. M., eds. (1993) DNA Sequencing Protocols. Humana Press, Totowa, N.J., USA, Brown, T. A. (1994) DNA Sequencing: The Basics. IRL Press, Oxford, GB and Ansorge, W., Voss, H. and Zimmermann, J., eds. (1997) DNA Sequencing Strategies: Automated and Advanced Approaches. Wiley, New York, N.Y., U.S.). To avoid ssDNA isolation, direct sequencing of double-stranded (ds) DNA was developed. However, the robustness of direct sequencing denatured dsDNA is often compromised by poor sequence readability and/or spurious sequence data resulting from non-specific mispriming. For this reason, isothermal dideoxy sequencing of dsDNA is normally limited to constructs of less than 50 kb. Thermal cycle sequencing overcomes this size limitation thereby allowing multimegabase-template dsDNA to be directly sequenced (See: Heiner, C. R., Hunkapiller, K. L., Chen, S.-M., Glass, J. I. and Chen, E. Y. (1998) Genome Res. 8, 557-561). However, careful choice of various parameters and operation with the thermal cycler is requisite for cycle sequencing.
Therefore, it is highly desirable to develop isothermal methods for sequencing non-denatured dsDNA. To this end, solid phase sequencing of dsDNA restriction fragments by strand displacement or nick translation was recently described (See: Fu, D.-J., Koster, H., Smith, C. L. and Cantor, C. R. (1997) Nucleic Acids Res. 25, 677-679). Still, this approach cannot be applied for direct sequencing of long DNA or closed circular dsDNA.
C. Nucleic Acid Comprising Topologically Linked Structures.
DNA is well known to adopt various topological (and pseudotopological) structures like knots, catenanes, Borromean rings and pseudorotaxanes. (See: M. D. Frank-Kamenetskii, J. Mol. Struct. (Theochem) 1995, 336, 235-243; N. C. Seeman, Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-248; K. Ryan, E. T. Kool, Chem. & Biol. 1998, 5, 59-67; N. C. Seeman, Angew. Chem. 1998, 110, 3408-3428; and Angew. Chem. Int. Ed. Engl. 1998, 37, 3220-3238). It has long been recognized that DNA topology plays a crucial role in such fundamental biological phenomena as DNA supercoiling and topoisomerization (See M. D. Frank-Kamenetskii, Unraveling DNA: The most important molecule of life, Addison-Wesley, Reading, Mass., USA 1997, p. 214; and R. Sinden, DNA Structure and Function, Academic Press, San Diego, Calif., USA 1994, p. 398). Another reason for a considerable interest in higher order DNA topology structures stems from the realization that DNA topological and pseudotopological forms may provide stable and sequence-specific targeting of DNA. Accordingly, highly localized DNA detection and precise spatial positioning of various ligands on DNA scaffold becomes possible. This may lead to new applications in molecular biotechnology, gene therapy and in the emerging field of DNA nanotechnology (See: N. C. Seeman, Acc. Chem. Res. 1997, 30, 357-363; b) C. M. Niemeyer, Angew. Chem. 1997, 109, 603-606; and Angew. Chem. Int. Ed. EngL. 1997, 36, 585-587).
One of promising DNA pseudotopological constructions is the DNA padlock consisting of a long single-stranded (ss) DNA molecule forming a pseudorotaxane with a short cyclic oligodeoxynudeotide (CODN) (See: M. Nilsson, H. Malmgren, M. Samiotaki, M. Kwiatkowski, B. P. Chowdhary, U. Landegren, Science 1994, 265, 2085-2088; M. Nilsson, K. Krejci, J. Koch, M. Kwiatkowski, P. Gustavsson, U. Landegren, Nature Gen. 1997, 16, 252-254; P. M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D. C. Thomas, D. C. Ward, Nature Gen. 1998, 19, 225-232; and J. Baneer, M. Nilsson, M. Mendel-Hartvig, U. Landegren, Nucleic Acids Res. 1998, 26, 5073-5078). Another interesting pseudorotaxane-type structure is the sliding clamp which contains a short cODN threaded on double-stranded (ds) DNA (See: K Ryan, E. T. Kool, Chem. & Biol. 1998, 5, 59-67; d) N. C. Seeman, Angew. Chem. 1998, 110, 3408-3428). Notwithstanding the value of the indicated pseudotopological structures for DNA labeling, note that in these constructions the CODN tag is allowed to slide along the target for considerable distances thereby compromising the precision of spatial positioning of the label.